[gmx-users] custom forcefields or a new forcefields

Gareth Tribello gareth.tribello at gmail.com
Thu Apr 1 15:25:11 CEST 2010


Basically you can provide a file in which you calculate the values of your
potential function for different values of r.  You will have to write a
small program to create the table file yourself I think.  The details of
what should be in it are described in section 6.7.2 of the manual but
briefly gromacs treats your forcefield as follows:

V(r) = (q_i q_j / 4 pi eps_0 ) f(r) + A g(r) + C h(r)

Your table should have seven columns which are:

r, f(r) , f'(r) , g(r), g'(r) , h(r), h'(r)

Gromacs will then get itself the A and C from the topol.top file.
 (incidentally your mix type in the initial defaults line should be 1).  The
spacing between r values will depend on whether you are using a single or
double precision version of gromacs.

As an example if you were using Lennard Jones with a coulomb interaction

f(r) = 1/r
g(r) = -1/r**6
h(r) = 1/r**12

You then need to put the tables you are using in the directory in which you
are running gromacs.


On Thu, Apr 1, 2010 at 12:08 PM, DreamCatcher <huangshuping1987 at gmail.com>wrote:

> Message: 5
> Date: Thu, 01 Apr 2010 16:30:44 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] custom forcefields or a new forcefields
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BB42F84.9050703 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> On 01/04/10 16:20, DreamCatcher wrote:
> > Hello gmx-users,
> >         I have just look through the mail-list to find this
> > http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.htmlconcerned
> > on the develop of a new force field.
> >         It seems that If I wanna use a force field haven't been
> > incooperate into the gromacs' extant version, What I need to do only is
> > to make some new files with suffixes like .rtp / .hdb / nb.itp / bon.itp
> > to contain the new force field parameters.
> Yes.
> > This may certainly work out
> > for pdb2gmx programme, But will it also work out for another programmes
> > like mdrun?
> Well, it will, because pdb2gmx builds topologies that grompp can parse
> into input for mdrun.
> > Cause maybe the forcefield potential function are different
> > from any other forcefileds contained in the gromacs. Then what others
> > can I do to finally introduce a totally new force field to gromacs?
> Have a look at all the possibilities GROMACS already knows about in
> chapter 4, and consider also the use of table-lookups for two-body
> functions (manual 6.7.2). IIRC many-bodied functions won't work yet.
> Mark
> ------------------------------
> Hey Mark,
>        Thanks very much for your benevolence. Another question, How can I
> set up a new functions? Where should they be located? What do you mean when
> you talk about "table-lookups  for two-body functions"? Where should the
> lookups take place?
>        When I use "man mdrun" to find a "-table" option for table-lookup,
> it obviously indicates an input file **.xvg, What can **.xvg file do? How
> should it be created? What is the content in it?
>        Thank a lot and thanks in advance!
> celeste
> 2010-4-1
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